[English] 日本語
Yorodumi
- PDB-1qjb: 14-3-3 ZETA/PHOSPHOPEPTIDE COMPLEX (MODE 1) -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: PDB / ID: 1qjb
Title14-3-3 ZETA/PHOSPHOPEPTIDE COMPLEX (MODE 1)
Components
  • 14-3-3 PROTEIN ZETA/DELTA
  • PHOSPHOPEPTIDE
KeywordsKINASE INHIBITOR/PEPTIDE / KINASE INHIBITOR-PEPTIDE COMPLEX / SIGNAL TRANSDUCTION
Function / homology
Function and homology information


KSRP (KHSRP) binds and destabilizes mRNA / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / protein localization => GO:0008104 / Golgi reassembly / Rap1 signalling / TP53 Regulates Metabolic Genes / regulation of synapse maturation / Interleukin-3, Interleukin-5 and GM-CSF signaling ...KSRP (KHSRP) binds and destabilizes mRNA / NOTCH4 Activation and Transmission of Signal to the Nucleus / Regulation of localization of FOXO transcription factors / Activation of BAD and translocation to mitochondria / protein localization => GO:0008104 / Golgi reassembly / Rap1 signalling / TP53 Regulates Metabolic Genes / regulation of synapse maturation / Interleukin-3, Interleukin-5 and GM-CSF signaling / NOTCH4 Activation and Transmission of Signal to the Nucleus / establishment of Golgi localization / Rap1 signalling / negative regulation of protein localization to nucleus / KSRP (KHSRP) binds and destabilizes mRNA / GP1b-IX-V activation signalling / Regulation of localization of FOXO transcription factors / host cell membrane / Interleukin-3, Interleukin-5 and GM-CSF signaling / phosphoserine residue binding / Activation of BAD and translocation to mitochondria / cellular response to glucose starvation / SARS-CoV-2 targets host intracellular signalling and regulatory pathways / Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex / SARS-CoV-1 targets host intracellular signalling and regulatory pathways / RHO GTPases activate PKNs / negative regulation of TORC1 signaling / viral process / negative regulation of innate immune response / protein sequestering activity / regulation of ERK1 and ERK2 cascade / Translocation of SLC2A4 (GLUT4) to the plasma membrane / Deactivation of the beta-catenin transactivating complex / TP53 Regulates Metabolic Genes / Negative regulation of NOTCH4 signaling / melanosome / blood microparticle / DNA-binding transcription factor binding / vesicle / transmembrane transporter binding / membrane => GO:0016020 / cadherin binding / protein phosphorylation / focal adhesion / glutamatergic synapse / ubiquitin protein ligase binding / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / signal transduction / extracellular space / RNA binding / extracellular exosome / nucleoplasm / identical protein binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site ...Small/middle T-antigen / Small/middle T-antigen superfamily / T-antigen specific domain / 14-3-3 domain / Delta-Endotoxin; domain 1 / DnaJ molecular chaperone homology domain / Chaperone J-domain superfamily / DnaJ domain / 14-3-3 proteins signature 2. / 14-3-3 protein, conserved site / 14-3-3 proteins signature 1. / 14-3-3 protein / 14-3-3 homologues / 14-3-3 domain / 14-3-3 domain superfamily / 14-3-3 protein / Up-down Bundle / Mainly Alpha
Similarity search - Domain/homology
Middle T antigen / 14-3-3 protein zeta/delta / 14-3-3 protein zeta/delta
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsRittinger, K. / Budman, J. / Xu, J. / Volinia, S. / Cantley, L.C. / Smerdon, S.J. / Gamblin, S.J. / Yaffe, M.B.
CitationJournal: Mol.Cell / Year: 1999
Title: Structural Analysis of 14-3-3 Phosphopeptide Complexes Identifies a Dual Role for the Nuclear Export Signal of 14-3-3 in Ligand Binding
Authors: Rittinger, K. / Budman, J. / Xu, J. / Volinia, S. / Cantley, L.C. / Smerdon, S.J. / Gamblin, S.J. / Yaffe, M.B.
History
DepositionJun 23, 1999Deposition site: PDBE / Processing site: PDBE
SupersessionSep 15, 1999ID: 14PS
Revision 1.0Sep 15, 1999Provider: repository / Type: Initial release
Revision 1.1Sep 5, 2012Group: Database references / Derived calculations ...Database references / Derived calculations / Non-polymer description / Other / Structure summary / Version format compliance
Revision 1.2Feb 28, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant

-
Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

-
Assembly

Deposited unit
A: 14-3-3 PROTEIN ZETA/DELTA
B: 14-3-3 PROTEIN ZETA/DELTA
Q: PHOSPHOPEPTIDE
S: PHOSPHOPEPTIDE


Theoretical massNumber of molelcules
Total (without water)57,4944
Polymers57,4944
Non-polymers00
Water7,080393
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4210 Å2
ΔGint-26.8 kcal/mol
Surface area23480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)68.350, 71.980, 131.000
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

-
Components

#1: Protein 14-3-3 PROTEIN ZETA/DELTA


Mass: 27777.092 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PKK233 / Production host: Escherichia coli DH5[alpha] (bacteria) / Variant (production host): F' Iq / References: UniProt: P29312, UniProt: P63104*PLUS
#2: Protein/peptide PHOSPHOPEPTIDE /


Mass: 969.935 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) HOMO SAPIENS (human) / References: UniProt: P0DOJ9*PLUS
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 393 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsCHAINS S AND Q ARE DERIVED FROM THE SEQUENCE, VMRSHSYPPT, FOUND IN MOUSE POLYOMAVIRUS (STRAIN 3) ...CHAINS S AND Q ARE DERIVED FROM THE SEQUENCE, VMRSHSYPPT, FOUND IN MOUSE POLYOMAVIRUS (STRAIN 3) MIDDLE T ANTIGEN (SWS: TAMI_POVM3, P03076)

-
Experimental details

-
Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

-
Sample preparation

CrystalDensity Matthews: 2.8 Å3/Da / Density % sol: 56 %
Crystal growpH: 6.2
Details: COMPLEX WAS CRYSTALLIZED FROM 100 MM MES, PH 6.2, 20 MM MGCL2, 20% ISOPROPANOL AND 15% PEG 4000. IMPROVED CRYSTALS BY MICRO- AND MACROSEEDING INTO 100 MM MES, PH 6.2, 20 MM MGCL2, 15-17% ...Details: COMPLEX WAS CRYSTALLIZED FROM 100 MM MES, PH 6.2, 20 MM MGCL2, 20% ISOPROPANOL AND 15% PEG 4000. IMPROVED CRYSTALS BY MICRO- AND MACROSEEDING INTO 100 MM MES, PH 6.2, 20 MM MGCL2, 15-17% ISOPROPANOL A 12% PEG 4000.
Crystal grow
*PLUS
Temperature: 4 ℃ / Method: vapor diffusion, hanging drop / Details: used to seeding
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
1100 mMMES1reservoir
220 mM1reservoirMgCl2
315-17 %isopropanol1reservoir
412 %PEG40001reservoir

-
Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Details: MIRROR
RadiationMonochromator: SINGLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.488 Å / Relative weight: 1
ReflectionResolution: 2→15 Å / Num. obs: 37059 / % possible obs: 83.5 % / Observed criterion σ(I): 2 / Redundancy: 2 % / Rmerge(I) obs: 0.059 / Net I/σ(I): 13.3
Reflection shellResolution: 2→2.09 Å / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 2.1 / % possible all: 41.6
Reflection shell
*PLUS
% possible obs: 41.6 %

-
Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 14-3-3 ZETA

Resolution: 2→15 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: THE C-TERMINAL RESIDUES FOR CHAINS A AND B WERE NOT SEEN IN THE DENSITY MAPS
RfactorNum. reflection% reflectionSelection details
Rfree0.288 -5 %RANDOM
Rwork0.21 ---
obs-37059 83.5 %-
Refinement stepCycle: LAST / Resolution: 2→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3800 0 0 393 4193
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0120.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.21
Solvent computation
*PLUS
Displacement parameters
*PLUS

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more